Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 56 of 316
Found at i:16525990 original size:52 final size:52
Alignment explanation
Indices: 16525912--16526019 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
16525902 TGAAATGCCC
16525912 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCG-TT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAA-CCGATT
* *
16525964 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCGATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCGATT
16526016 ATCA
1 ATCA
16526020 ATTTGTACCA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 3 0.06
52 50 0.94
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCGATT
Found at i:16527550 original size:41 final size:41
Alignment explanation
Indices: 16527480--16527654 Score: 235
Period size: 41 Copynumber: 4.3 Consensus size: 41
16527470 ATAAAATTTT
* * ***
16527480 CTAGGC-ATAAAGCCTAGTACAATACACCGGCACGGAGCCTG
1 CTAGGCAAT-AAGCCTAATATAATACACCGGCATAAAGCCTG
* * *
16527521 CTACGCAATAGGCCTAATATAATATACCGGCATAAAGCCTG
1 CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
*
16527562 CTAGGCAATAAGCCTGATATAATACACCGGCATAAAGCCTG
1 CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
* *
16527603 CTAGGCAATAAGCCTGATATAATACACTGGCATAAAGCCTG
1 CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
16527644 CTAGGCAATAA
1 CTAGGCAATAA
16527655 AACCTGAATA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 118 0.98
42 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (41 bp):
CTAGGCAATAAGCCTAATATAATACACCGGCATAAAGCCTG
Found at i:16538626 original size:13 final size:13
Alignment explanation
Indices: 16538608--16538632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16538598 TGTGGGTGCA
16538608 CATGGCCGTGTCG
1 CATGGCCGTGTCG
16538621 CATGGCCGTGTC
1 CATGGCCGTGTC
16538633 TTGCTTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CATGGCCGTGTCG
Found at i:16540753 original size:13 final size:13
Alignment explanation
Indices: 16540735--16540763 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16540725 TTTAGTTTAA
16540735 TTAGTTAATTAGT
1 TTAGTTAATTAGT
16540748 TTAGTTAATTAGT
1 TTAGTTAATTAGT
16540761 TTA
1 TTA
16540764 ATAAACAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:16542857 original size:27 final size:27
Alignment explanation
Indices: 16542799--16542905 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 27
16542789 TGGCTGCAAA
* *
16542799 AACAGATAA-TGTGACAGAGTCACCAG
1 AACAGATAATTGTGGCAGAGCCACCAG
* **
16542825 ATACAGATAATCGTGGCAGAGCCTTCAG
1 A-ACAGATAATTGTGGCAGAGCCACCAG
*
16542853 AACAGA-AATATGTTGCAGAGCCACCAG
1 AACAGATAAT-TGTGGCAGAGCCACCAG
* *
16542880 ATCAGATAATTGTGGCATAGCCACCA
1 AACAGATAATTGTGGCAGAGCCACCA
16542906 AGACGCTTCC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
26 4 0.06
27 45 0.69
28 16 0.25
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (27 bp):
AACAGATAATTGTGGCAGAGCCACCAG
Found at i:16543177 original size:8 final size:8
Alignment explanation
Indices: 16543164--16543192 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
16543154 TACCGAATTG
16543164 GGCCCGTT
1 GGCCCGTT
16543172 GGCCCGTT
1 GGCCCGTT
16543180 GGCCCGTT
1 GGCCCGTT
16543188 GGCCC
1 GGCCC
16543193 ATTAACCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.41, G:0.38, T:0.21
Consensus pattern (8 bp):
GGCCCGTT
Found at i:16549552 original size:40 final size:40
Alignment explanation
Indices: 16549461--16549595 Score: 155
Period size: 41 Copynumber: 3.3 Consensus size: 40
16549451 ACATAAAATT
* *
16549461 TGCTAGGC-ATAAAGCCTAGTATAATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTAATATAATACACCGGCATA-AGCC
* * * *
16549502 TACTAGGCAATAGGTCTAATATAATATACCGGCATAAGCC
1 TGCTAGGCAATAAGCCTAATATAATACACCGGCATAAGCC
* *
16549542 TGCTAGGCAATAAGCCTGATATAATACAGCGGCATAAAGCC
1 TGCTAGGCAATAAGCCTAATATAATACACCGGCAT-AAGCC
*
16549583 TGCTAGTCAATAA
1 TGCTAGGCAATAA
16549596 AGCCCAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 33 0.42
41 44 0.56
42 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (40 bp):
TGCTAGGCAATAAGCCTAATATAATACACCGGCATAAGCC
Found at i:16560625 original size:16 final size:16
Alignment explanation
Indices: 16560606--16560636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16560596 CTTCTTCACT
16560606 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
16560622 TACTTACTTACTTAA
1 TACTCACTTACTTAA
16560637 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:16560642 original size:20 final size:20
Alignment explanation
Indices: 16560603--16560642 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16560593 AAACTTCTTC
* *
16560603 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
16560623 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
16560643 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:16561011 original size:55 final size:54
Alignment explanation
Indices: 16560899--16561076 Score: 184
Period size: 55 Copynumber: 3.3 Consensus size: 54
16560889 CATGCCTCAA
* * *
16560899 CATGGTCTTACATGGTATCC-TAGCCTTATG-AA-CTCACCAATGCCATGCCTTGG
1 CATGGTCTTACATGGGA-CCTTTGCCTTA-GAAACCTTACCAATGCCATGCCTTGG
* * * *
16560952 CATGGTCTTACATGGGACCTTTGACTTCTAGAAA-CTTATCAATGCCATGTCTTGA
1 CATGGTCTTACATGGGACCTTTG-CCT-TAGAAACCTTACCAATGCCATGCCTTGG
** * *
16561007 CATGGTCTTACATGATATCTTTGCCTTAGAAACCTTACCAATTTCCATGCCTTGG
1 CATGGTCTTACATGGGACCTTTGCCTTAGAAACCTTACCAA-TGCCATGCCTTGG
16561062 CATGGTCTTACATGG
1 CATGGTCTTACATGG
16561077 TATCCTTAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 24 0.23
54 12 0.12
55 65 0.63
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (54 bp):
CATGGTCTTACATGGGACCTTTGCCTTAGAAACCTTACCAATGCCATGCCTTGG
Found at i:16567815 original size:48 final size:47
Alignment explanation
Indices: 16567661--16567825 Score: 192
Period size: 48 Copynumber: 3.5 Consensus size: 47
16567651 TTCAGTTATG
* *
16567661 TATTGGCACTTTGTGTGCGAGATTGAAATAGCTTCGACTACATATATA
1 TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGACTATATATA-A
* *
16567709 TATTGGCACTTAGTGTGCGAGACTAAAATAGCTTCGACTATATA-AA
1 TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGACTATATATAA
* *
16567755 TATTGGCACTTAGTGCGCGTA-ATTGAGATAGCTTCTG-CTATATATACA
1 TATTGGCACTTAGTGTGCG-AGATTGAAATAGCTTC-GACTATATATA-A
* * *
16567803 CATTGGCACTTAGCGTACGAGAT
1 TATTGGCACTTAGTGTGCGAGAT
16567826 CAATAGAGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
46 37 0.37
47 5 0.05
48 58 0.58
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (47 bp):
TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGACTATATATAA
Found at i:16567839 original size:94 final size:94
Alignment explanation
Indices: 16567661--16567843 Score: 219
Period size: 94 Copynumber: 1.9 Consensus size: 94
16567651 TTCAGTTATG
* * * * * *
16567661 TATTGGCACTTTGTGTGCGAGATTGAAATAGCTTCGACTACATATATATATTGGCACTTAGTGTG
1 TATTGGCACTTAGTGCGCGAGATTGAAATAGCTTCGACTACATATACACATTGGCACTTAGCGTA
*
16567726 CGAGACTAAAATAGCTTCGACTATATAAA
66 CGAGACTAAAAGAGCTTCGACTATATAAA
* *
16567755 TATTGGCACTTAGTGCGCGTA-ATTGAGATAGCTTCTG-CTATATATACACATTGGCACTTAGCG
1 TATTGGCACTTAGTGCGCG-AGATTGAAATAGCTTC-GACTACATATACACATTGGCACTTAGCG
* *
16567818 TACGAGA-TCAATAGAGTTTCGACTAT
64 TACGAGACT-AAAAGAGCTTCGACTAT
16567844 TTATTTGGCA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
93 1 0.01
94 72 0.96
95 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (94 bp):
TATTGGCACTTAGTGCGCGAGATTGAAATAGCTTCGACTACATATACACATTGGCACTTAGCGTA
CGAGACTAAAAGAGCTTCGACTATATAAA
Found at i:16571274 original size:16 final size:16
Alignment explanation
Indices: 16571255--16571285 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16571245 CTTCGTCACT
16571255 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
16571271 TACTTACTTACTTAA
1 TACTCACTTACTTAA
16571286 TGAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:16571291 original size:20 final size:20
Alignment explanation
Indices: 16571252--16571291 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16571242 AAACTTCGTC
* *
16571252 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATGAAAT
*
16571272 ACTTACTTACTTAATGAAAT
1 ACTTACTCACTTAATGAAAT
16571292 TTATTAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATGAAAT
Found at i:16571640 original size:55 final size:55
Alignment explanation
Indices: 16571495--16571704 Score: 232
Period size: 55 Copynumber: 3.9 Consensus size: 55
16571485 GTATCCTTTT
* * *
16571495 GAAACTTACCATTGACATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAT-
1 GAAACTTACCAATGACATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * ** *
16571549 G-AACTCACCAATGCCATGCCTTGGTATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAAACTTACCAATGACATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* * *
16571603 GAAACTTATCAATGACATGTCTTGACATGGTCTTACATGATATCCTTGCC-T-TA
1 GAAACTTACCAATGACATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
** *
16571656 GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 GAAA-CTTACCAA-TGACATGCCTTGACATGGTCTTACATGGTATCCTT
16571705 AAACCCCAAT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
52 2 0.02
53 47 0.37
54 10 0.08
55 67 0.52
56 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (55 bp):
GAAACTTACCAATGACATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:16574329 original size:26 final size:27
Alignment explanation
Indices: 16574279--16574332 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
16574269 TTGCCTCAAG
16574279 TTCAAATCTTTTTGAGTCATCAAATAT
1 TTCAAATCTTTTTGAGTCATCAAATAT
16574306 TTCAAA-CTTTTGTGA-TCAGT-AAATAT
1 TTCAAATCTTTT-TGAGTCA-TCAAATAT
16574332 T
1 T
16574333 CAGCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (27 bp):
TTCAAATCTTTTTGAGTCATCAAATAT
Found at i:16586417 original size:26 final size:26
Alignment explanation
Indices: 16586381--16586431 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
16586371 TCGCAACCCG
16586381 ACTGACACTAGCATTTCTAGGATATA
1 ACTGACACTAGCATTTCTAGGATATA
*
16586407 ACTGGCACTAGCATTTCTAGGATAT
1 ACTGACACTAGCATTTCTAGGATAT
16586432 CTCGGAGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (26 bp):
ACTGACACTAGCATTTCTAGGATATA
Found at i:16588097 original size:41 final size:43
Alignment explanation
Indices: 16588039--16588131 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
16588029 TTTTTAGTTC
* * *
16588039 GTCTGGGACATTGGCATCG-TATTTGATTTCGTGTAAGAACCT
1 GTCTGGGACAGTGGCATCGATATTTGATTACATGTAAGAACCT
16588081 GTCT-GGACAGTGGCATCGATATTTGATTACATGTAAG-ACCAT
1 GTCTGGGACAGTGGCATCGATATTTGATTACATGTAAGAACC-T
*
16588123 GTTTGGGAC
1 GTCTGGGAC
16588132 GTTGGAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 16 0.36
42 24 0.55
43 4 0.09
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GTCTGGGACAGTGGCATCGATATTTGATTACATGTAAGAACCT
Found at i:16588469 original size:48 final size:48
Alignment explanation
Indices: 16588414--16588516 Score: 206
Period size: 48 Copynumber: 2.1 Consensus size: 48
16588404 TGGCTAAGGA
16588414 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
1 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
16588462 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
1 GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
16588510 GTATATG
1 GTATATG
16588517 GCTTACTAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (48 bp):
GTATATGTATATTATGATGCTTATATGTTTATATTGTTAAGTTTATTT
Found at i:16596755 original size:22 final size:22
Alignment explanation
Indices: 16596680--16596756 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
16596670 CATGGAAGGG
*
16596680 GGAGACACAC--CCATGTGAG-
1 GGAGACACACGGCCGTGTGAGA
*
16596699 GGA-ACACACGCCCGTGTGAGA
1 GGAGACACACGGCCGTGTGAGA
* *
16596720 GGAGGCACACGGCCGTGTGGGA
1 GGAGACACACGGCCGTGTGAGA
* *
16596742 GGAGATACATGGCCG
1 GGAGACACACGGCCG
16596757 AAGGCACATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.13
19 3 0.06
20 8 0.17
21 3 0.06
22 27 0.57
ACGTcount: A:0.26, C:0.25, G:0.39, T:0.10
Consensus pattern (22 bp):
GGAGACACACGGCCGTGTGAGA
Found at i:16597510 original size:3 final size:3
Alignment explanation
Indices: 16597502--16597527 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16597492 AAAATAGGAA
16597502 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
16597528 AACTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16599855 original size:6 final size:6
Alignment explanation
Indices: 16599844--16599872 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
16599834 ATATCAATCC
16599844 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
16599873 GAATGCCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:16601991 original size:25 final size:25
Alignment explanation
Indices: 16601955--16602010 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
16601945 GTGTTCTTGG
*
16601955 TTCTTTTTTATTTT-TATTTAGTTT-T
1 TTCTTTTGTATTTTCT-TTTA-TTTCT
16601980 TTCTTTTGTATTTTCTTTTATTTCT
1 TTCTTTTGTATTTTCTTTTATTTCT
16602005 TTCTTT
1 TTCTTT
16602011 CCCTTCGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.11
25 24 0.86
26 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.79
Consensus pattern (25 bp):
TTCTTTTGTATTTTCTTTTATTTCT
Found at i:16603000 original size:3 final size:3
Alignment explanation
Indices: 16602994--16603085 Score: 62
Period size: 3 Copynumber: 30.7 Consensus size: 3
16602984 CATCATCATC
* * *
16602994 ATT ATT ATT GA-T ATT ATT ATT ATT ATT ATT ATT ATT GTT GTT GTT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
16603039 ACTT TTT GTC ACT ATT GTC ATT ATT A-T ATT ATT ACT ATT ATT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16603084 AT
1 AT
16603086 ACTTATATTC
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.04
3 64 0.91
4 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:16606329 original size:13 final size:13
Alignment explanation
Indices: 16606313--16606337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16606303 CCATTACCAG
16606313 AAATAATAATAAC
1 AAATAATAATAAC
16606326 AAATAATAATAA
1 AAATAATAATAA
16606338 ATATCTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:16606655 original size:2 final size:2
Alignment explanation
Indices: 16606648--16606707 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
16606638 TCTCCATGCA
16606648 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
16606690 CT CT CT CG CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
16606708 TTTCTGGCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:16620286 original size:23 final size:23
Alignment explanation
Indices: 16620260--16620310 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
16620250 TGATTTTTAA
*
16620260 ATTTAGAATTATTTAGTGATAGT
1 ATTTAGAATTATTTAGTGATAAT
16620283 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
16620306 ATTTA
1 ATTTA
16620311 AGAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:16633607 original size:6 final size:6
Alignment explanation
Indices: 16633596--16633634 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
16633586 TTTGAATCCC
16633596 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
16633635 CCCTTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:16642475 original size:93 final size:93
Alignment explanation
Indices: 16642368--16642536 Score: 293
Period size: 93 Copynumber: 1.8 Consensus size: 93
16642358 CATAAGTGAG
* * *
16642368 CTCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGA
1 CTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAACGA
16642433 GCTCGGATGCCTAGTTACATCTCTCGAA
66 GCTCGGATGCCTAGTTACATCTCTCGAA
*
16642461 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAACGA
1 CTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAACGA
*
16642526 GTTCGGATGCC
66 GCTCGGATGCC
16642537 CAAGCATCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
CTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAACGA
GCTCGGATGCCTAGTTACATCTCTCGAA
Found at i:16642532 original size:46 final size:46
Alignment explanation
Indices: 16642357--16642532 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
16642347 TGTAACCCGC
* * *
16642357 CCATAAGTGAGCTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
16642403 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
16642449 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
16642496 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
16642533 TGCCCAAGCA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:16646414 original size:13 final size:13
Alignment explanation
Indices: 16646396--16646435 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
16646386 AAAATAATCG
16646396 CACACGGGCGTGT
1 CACACGGGCGTGT
16646409 CACACGGGCGTGT
1 CACACGGGCGTGT
16646422 CACACGGGCGTGT
1 CACACGGGCGTGT
16646435 C
1 C
16646436 CCTCCCGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:16650187 original size:47 final size:47
Alignment explanation
Indices: 16650127--16650288 Score: 149
Period size: 47 Copynumber: 3.5 Consensus size: 47
16650117 TCCATAAGTG
* *
16650127 AACTCGGACTCAACTTAACGAGCTCGGATGCCTAGTTACATCTCACA
1 AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACA
* * * * *
16650174 AACTCAGACTCAACTCAATGAGTTC--A-GAC--GTTCGCATC-CATAA
1 AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACATCTCA-CA
*
16650217 GTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCGT-ACG
1 ---AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATC-TCACA
16650267 AACTCAGACTCAACTCAACGAG
1 AACTCAGACTCAACTCAACGAG
16650289 TTCAGACGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
42 5 0.06
43 5 0.06
44 2 0.02
45 1 0.01
46 23 0.26
47 43 0.48
48 1 0.01
49 2 0.02
50 4 0.04
51 4 0.04
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (47 bp):
AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACA
Found at i:16650189 original size:93 final size:93
Alignment explanation
Indices: 16650081--16650344 Score: 415
Period size: 93 Copynumber: 2.8 Consensus size: 93
16650071 CCCATAAGCG
* * * * *
16650081 AACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTTAA
1 AACTCAGACTCAACTCAACGAG-TTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
16650145 CGAGCTCGGATGCCTAGTTACATC-TCACA
65 CGAGCTCGGATGCCTAGTTACATCGT-ACA
*
16650174 AACTCAGACTCAACTCAATGAGTTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
*
16650239 GAGCTCGGATGCCTAGTTACATCGTACG
66 GAGCTCGGATGCCTAGTTACATCGTACA
16650267 AACTCAGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
* *
16650332 AAGTTCGGATGCC
66 GAGCTCGGATGCC
16650345 CAAATATCCT
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
92 2 0.01
93 156 0.98
94 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCGTACA
Found at i:16650337 original size:46 final size:46
Alignment explanation
Indices: 16650072--16650337 Score: 206
Period size: 46 Copynumber: 5.7 Consensus size: 46
16650062 TGTAACCTGC
* * * *
16650072 CCATAAGCGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAG-TTCAGACGTTCGCAT
* * * * *
16650118 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC--A-GAC--GTTCGCAT
* *
16650168 CTCA-CA---AACTCAGACTCAACTCAATGAGTTCAGACGTTCGCAT
1 C-CATAAGTGAACTCAGACTCAACTCAACGAGTTCAGACGTTCGCAT
* * * * * *
16650211 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAGACG-TTCGCAT
* *
16650257 ACAT-CGTACGAACTCAGACTCAACTCAACGAGTTCAGACGTTCGCAT
1 CCATAAGT--GAACTCAGACTCAACTCAACGAGTTCAGACGTTCGCAT
*
16650304 CCATAAGTGAACTCAGACTCAACTCAACAAGTTC
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC
16650338 GGATGCCCAA
Statistics
Matches: 171, Mismatches: 32, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
42 5 0.03
43 5 0.03
44 2 0.01
45 4 0.02
46 86 0.50
47 55 0.32
48 2 0.01
49 2 0.01
50 5 0.03
51 5 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAGACGTTCGCAT
Found at i:16661025 original size:45 final size:45
Alignment explanation
Indices: 16660961--16661181 Score: 306
Period size: 45 Copynumber: 5.0 Consensus size: 45
16660951 ATATCGTACA
* *
16660961 ATACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCAGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
16661006 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
** **
16661051 ATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATAACGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* *
16661096 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAA
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* * *
16661141 ATGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGTCGGTGA
1 AT-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
16661182 ATGAATTCGG
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 9 0.06
43 17 0.11
44 5 0.03
45 127 0.80
46 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (45 bp):
ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
Found at i:16661741 original size:16 final size:18
Alignment explanation
Indices: 16661710--16661742 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
16661700 AACTCGTCAC
16661710 ACTATCTATCATTTTGGT
1 ACTATCTATCATTTTGGT
16661728 ACTA-CTAT-ATTTTGG
1 ACTATCTATCATTTTGG
16661743 AGCTAGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (18 bp):
ACTATCTATCATTTTGGT
Found at i:16667225 original size:80 final size:80
Alignment explanation
Indices: 16667045--16667305 Score: 294
Period size: 80 Copynumber: 3.3 Consensus size: 80
16667035 TATTCGAATG
* * * * *
16667045 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAAACCCGAAGGC
*
16667110 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
16667126 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGGCA
* *
16667191 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * * *
16667206 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAAACCAGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGGCA
* * *
16667271 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
16667285 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
16667306 ATTACTTGAG
Statistics
Matches: 153, Mismatches: 25, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
78 14 0.09
79 14 0.09
80 94 0.61
81 31 0.20
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:16667268 original size:40 final size:40
Alignment explanation
Indices: 16667045--16667269 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
16667035 TATTCGAATG
** * *
16667045 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACT
* * * * * * *
16667086 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAG-CGACT
* * *
16667126 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
16667166 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
** * * *
16667206 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
* *
16667246 ACATCCGGGCTAAAACCAGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGC
16667270 CTTGTGCAAG
Statistics
Matches: 155, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 125 0.81
41 29 0.19
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
Found at i:16667268 original size:120 final size:120
Alignment explanation
Indices: 16667045--16667305 Score: 298
Period size: 120 Copynumber: 2.2 Consensus size: 120
16667035 TATTCGAATG
* * *
16667045 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * * * * * * *
16667110 ATTCGTGCGAGTTGCTATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGA-TT
66 ATTCATGCGAGTTGCCACATCCGGGCTAAAACCAGAAGGC-CTTGTGCAAG-GAGTT
* * *
16667166 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGG
* * *
16667229 CATTTATGCTAG-TGACCACATCCGGGCTAAAACCAGAAGGCCTTGTGCAAGTAGTT
65 CATTCATGCGAGTTG-CCACATCCGGGCTAAAACCAGAAGGCCTTGTGCAAGGAGTT
16667285 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAATCCCGAAG
16667306 ATTACTTGAG
Statistics
Matches: 119, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
118 15 0.13
119 19 0.16
120 54 0.45
121 31 0.26
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (120 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCCACATCCGGGCTAAAACCAGAAGGCCTTGTGCAAGGAGTT
Found at i:16674398 original size:40 final size:40
Alignment explanation
Indices: 16674304--16674528 Score: 240
Period size: 40 Copynumber: 5.6 Consensus size: 40
16674294 TATTCGAATG
*
16674304 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
16674345 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * * *
16674385 ATATCCGGGCTAAGACCCTAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
16674425 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
16674465 ATATCCAGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
16674505 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
16674529 CTTGTGCAAG
Statistics
Matches: 154, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.01
40 123 0.80
41 29 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:16674488 original size:80 final size:80
Alignment explanation
Indices: 16674304--16674564 Score: 294
Period size: 80 Copynumber: 3.3 Consensus size: 80
16674294 TATTCGAATG
* * * *
16674304 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
16674369 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * * *
16674385 ATATCCGGGCTAAGACCCTAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
16674450 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * * *
16674465 ATATCCAGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * *
16674530 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
16674544 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
16674565 ATTACTTGAG
Statistics
Matches: 152, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
78 14 0.09
79 14 0.09
80 93 0.61
81 31 0.20
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:16674518 original size:120 final size:120
Alignment explanation
Indices: 16674304--16674564 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
16674294 TATTCGAATG
* * *
16674304 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * * * * *
16674369 ATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCTAAGGCATTTGTGCTAGCGA-TT
66 ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAG-GAGTT
* *
16674425 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCAGG-CTAAG-TCCCGAAG
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACC-GGACTAAGAT-CCGAAG
* * *
16674487 GCATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGTAGTT
64 GCATTCATGCGAGTTG-CCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGGAGTT
16674544 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAATCCCGAAG
16674565 ATTACTTGAG
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
118 15 0.12
119 19 0.16
120 54 0.45
121 33 0.27
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (120 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGGAGTT
Found at i:16683476 original size:5 final size:5
Alignment explanation
Indices: 16683466--16683493 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16683456 GCAACTCACA
16683466 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16683494 GAATTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:16689256 original size:11 final size:11
Alignment explanation
Indices: 16689240--16689264 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16689230 AAAGTTTCCT
16689240 TTAGATAAGCA
1 TTAGATAAGCA
16689251 TTAGATAAGCA
1 TTAGATAAGCA
16689262 TTA
1 TTA
16689265 AGAAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (11 bp):
TTAGATAAGCA
Found at i:16690675 original size:25 final size:23
Alignment explanation
Indices: 16690641--16690686 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16690631 TTTTCTATTC
16690641 TCTCTCTTTTTTTACATTATAAG
1 TCTCTCTTTTTTTACATTATAAG
16690664 TCTCTCTTTTTTTACATTATAAG
1 TCTCTCTTTTTTTACATTATAAG
16690687 ATAATTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (23 bp):
TCTCTCTTTTTTTACATTATAAG
Found at i:16695144 original size:2 final size:2
Alignment explanation
Indices: 16695137--16695200 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
16695127 AATGCAGAAA
16695137 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16695179 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
16695201 GGAAAAAAGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16696937 original size:6 final size:7
Alignment explanation
Indices: 16696908--16696938 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16696898 AGGAAAAAAA
16696908 TTATATT
1 TTATATT
16696915 TTATATT
1 TTATATT
16696922 TTATATT
1 TTATATT
16696929 TTA-ATT
1 TTATATT
16696935 TTAT
1 TTAT
16696939 TTGATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:16697455 original size:32 final size:32
Alignment explanation
Indices: 16697390--16697458 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
16697380 TACAAATTTC
* *
16697390 TAATTTTTTTAATTTCAACTTTCATATTCAAT
1 TAATTTTTTTAATTTCAACTTACAAATTCAAT
16697422 TAATTTTTTTAATTTCAAC-TACAAGAATT-AAT
1 TAATTTTTTTAATTTCAACTTAC-A-AATTCAAT
16697454 TAATT
1 TAATT
16697459 AATTTAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
32 28 0.85
33 3 0.09
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (32 bp):
TAATTTTTTTAATTTCAACTTACAAATTCAAT
Found at i:16703475 original size:44 final size:44
Alignment explanation
Indices: 16703412--16703499 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
16703402 CCCAAACGAG
* *
16703412 AGTCTTACAAACATTCACAAATTTTAGCTTCCCGAGTGAGCCAT
1 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
16703456 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
1 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
16703500 TTTGACAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (44 bp):
AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
Found at i:16711212 original size:22 final size:24
Alignment explanation
Indices: 16711182--16711239 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
16711172 ACCATTAAAT
*
16711182 ATTTGTAATTAGT-ATTTTAAAAA
1 ATTTGTAATTAATAATTTTAAAAA
* *
16711205 ATTT-TAATTAATAATTTTAACAC
1 ATTTGTAATTAATAATTTTAAAAA
16711228 ATTTGTAATTAA
1 ATTTGTAATTAA
16711240 GCACCAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 16 0.53
24 7 0.23
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (24 bp):
ATTTGTAATTAATAATTTTAAAAA
Found at i:16712022 original size:32 final size:32
Alignment explanation
Indices: 16711986--16712051 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
16711976 GCAAGGTTTG
16711986 GAGAAAGGCTGCCACATTAACAATGACTACCT
1 GAGAAAGGCTGCCACATTAACAATGACTACCT
16712018 GAGAAAGGCTGCCACATTAACAATGACTACCT
1 GAGAAAGGCTGCCACATTAACAATGACTACCT
16712050 GA
1 GA
16712052 TAAATATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (32 bp):
GAGAAAGGCTGCCACATTAACAATGACTACCT
Found at i:16712453 original size:14 final size:14
Alignment explanation
Indices: 16712434--16712460 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16712424 GATCGTACGA
16712434 TACATAGACATAAT
1 TACATAGACATAAT
16712448 TACATAGACATAA
1 TACATAGACATAA
16712461 ACATACTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
TACATAGACATAAT
Found at i:16721623 original size:42 final size:40
Alignment explanation
Indices: 16721537--16721624 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
16721527 ATGATTGTTG
* *
16721537 AATTGAATATATATATATTGAGAAAATGTGTTTATTGTCA
1 AATTGAATATATATATATTGAGAAAATATGTATATTGTCA
* * * * *
16721577 AATTGAATATATGTTTATATGTGATAATATGTATATATGTGA
1 AATTGAATATATATATAT-TGAGAAAATATGTATAT-TGTCA
16721619 AATTGA
1 AATTGA
16721625 GACATTGGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 16 0.41
41 13 0.33
42 10 0.26
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.43
Consensus pattern (40 bp):
AATTGAATATATATATATTGAGAAAATATGTATATTGTCA
Found at i:16723888 original size:25 final size:26
Alignment explanation
Indices: 16723860--16723917 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
16723850 GGACACACCA
*
16723860 CAGCTCA-CATGAGTTTTCCGTTATT
1 CAGCTCAGCATGAGCTTTCCGTTATT
16723885 CAGCT-AGCATGAGCTTTCCGTTATT
1 CAGCTCAGCATGAGCTTTCCGTTATT
16723910 CAGCTCAG
1 CAGCTCAG
16723918 AAGAACTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 27 0.90
26 2 0.07
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (26 bp):
CAGCTCAGCATGAGCTTTCCGTTATT
Found at i:16737393 original size:69 final size:69
Alignment explanation
Indices: 16737311--16737470 Score: 209
Period size: 69 Copynumber: 2.3 Consensus size: 69
16737301 CTTTTTAAGT
* * *
16737311 ATTAAAATT--ATTTTTAATGAAATTAGTAAAGAATTGAGCTATAAGAGTATTCTTT-GCTCAAT
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAG-TCAAT
16737373 GAAGG
65 GAAGG
**
16737378 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATGTGAGTATTCTTTAGTCAATG
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAGTCAATG
**
16737443 TGGG
66 AAGG
* *
16737447 ATTAAAATTAACTTTTTTATGAAA
1 ATTAAAATTAAATTTTTAATGAAA
16737471 GTAGGGAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
67 9 0.11
69 71 0.88
70 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (69 bp):
ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAGTCAATG
AAGG
Found at i:16739432 original size:20 final size:20
Alignment explanation
Indices: 16739407--16739444 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16739397 AATTTTGGAT
*
16739407 TTATTTTTAATTATCTTTAA
1 TTATTTGTAATTATCTTTAA
*
16739427 TTATTTGTATTTATCTTT
1 TTATTTGTAATTATCTTT
16739445 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTGTAATTATCTTTAA
Found at i:16745910 original size:5 final size:5
Alignment explanation
Indices: 16745890--16745944 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
16745880 GGGCAACTCA
* * *
16745890 ATTTT ATTTT -TATTT ATTTT ATTTA ATTTA ATTTT ATTATT -TATT ATTTT
1 ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT
16745940 ATTTT
1 ATTTT
16745945 TGGATGTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 3 0.07
5 36 0.86
6 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:16745910 original size:15 final size:15
Alignment explanation
Indices: 16745890--16745945 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
16745880 GGGCAACTCA
16745890 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
*
16745905 ATTTTA-TTTAATTT
1 ATTTTATTTTTATTT
16745919 AATTTTATTATTTA-TT
1 -ATTTTATT-TTTATTT
16745935 ATTTTATTTTT
1 ATTTTATTTTT
16745946 GGATGTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.28
15 20 0.56
16 3 0.08
17 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTATTTTTATTT
Found at i:16748763 original size:96 final size:96
Alignment explanation
Indices: 16748585--16748767 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
16748575 TTTTTAAGAA
* ** *
16748585 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGGCTGTCATCTCTCTTCATGTCAAAAGGTTCG
1 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
*
16748650 ATATGTTCTTAAGAAAAATAAAAATTAGGAG
66 ATATGTTCTTAACAAAAATAAAAATTAGGAG
*** * * *
16748681 TATGTTGGGCTGAGTAATTGGGGTGAGGTGCTTGACTGTCATCTCTTTTCGCATCAAAAGGTTCA
1 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
*
16748746 ATATATT-TCTAACAAAAATAAA
66 ATATGTTCT-TAACAAAAATAAA
16748768 TAAATTAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.01
96 73 0.99
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (96 bp):
TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
ATATGTTCTTAACAAAAATAAAAATTAGGAG
Found at i:16748809 original size:8 final size:8
Alignment explanation
Indices: 16748796--16748820 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16748786 AAAAAAAGAG
16748796 AAAGAAAA
1 AAAGAAAA
16748804 AAAGAAAA
1 AAAGAAAA
16748812 AAAGAAAA
1 AAAGAAAA
16748820 A
1 A
16748821 TTAATAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:16749402 original size:14 final size:13
Alignment explanation
Indices: 16749383--16749420 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
16749373 ATTTAATATT
16749383 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
16749397 TAATTATTAAGGA
1 TAATTATTTAGGA
16749410 TAATTATTTAG
1 TAATTATTTAG
16749421 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:16749459 original size:20 final size:20
Alignment explanation
Indices: 16749434--16749473 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16749424 TAAATTTTAG
*
16749434 ATTTATTTTTAGTTATCTTT
1 ATTTATTTGTAGTTATCTTT
*
16749454 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTAGTTATCTTT
16749474 TAGAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTAGTTATCTTT
Found at i:16761563 original size:20 final size:20
Alignment explanation
Indices: 16761538--16761576 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16761528 AATTAGATTA
16761538 AAATTAGATACTGATAAATG
1 AAATTAGATACTGATAAATG
16761558 AAATTAGATACTGATAAAT
1 AAATTAGATACTGATAAAT
16761577 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (20 bp):
AAATTAGATACTGATAAATG
Found at i:16766827 original size:19 final size:19
Alignment explanation
Indices: 16766791--16766827 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16766781 TAATTAGGCT
* *
16766791 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
16766810 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
16766828 GAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:16768748 original size:23 final size:23
Alignment explanation
Indices: 16768704--16768748 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16768694 TTATAATTGA
* *
16768704 AAAGTGATTTTAAATTCGAAATG
1 AAAGTGATTTGAAATTCAAAATG
16768727 AAAGTGATTTGAGAATT-AAAAT
1 AAAGTGATTTGA-AATTCAAAAT
16768749 ACCTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (23 bp):
AAAGTGATTTGAAATTCAAAATG
Found at i:16775965 original size:41 final size:41
Alignment explanation
Indices: 16775920--16776148 Score: 297
Period size: 41 Copynumber: 5.6 Consensus size: 41
16775910 CAAACATTAC
16775920 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTTTAA
16775961 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
* *
16776002 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
* *
16776043 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
* *
16776084 GTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAA
1 GTCTAGCAGGCTTAA-TGCCGGTGATACAT--TTCAGACTTTAA
* **
16776125 GCCTAGCAGGCAAAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGA
16776149 ATCTGTTTAA
Statistics
Matches: 173, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
39 3 0.02
40 8 0.05
41 160 0.92
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
Found at i:16783936 original size:29 final size:30
Alignment explanation
Indices: 16783888--16783979 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
16783878 ATAATCATGT
16783888 TATCTGTTTCCGTTATATTCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
16783918 TATCTGTTT-CGTTATATTCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
* *
16783947 TATCTATTTCCGTTATATCCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
16783977 TAT
1 TAT
16783980 GTCATATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 28 0.47
30 31 0.53
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (30 bp):
TATCTGTTTCCGTTATATTCTTTTTATAAG
Found at i:16790017 original size:7 final size:7
Alignment explanation
Indices: 16790005--16790029 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16789995 TATTCATGTC
16790005 CCTTCCA
1 CCTTCCA
16790012 CCTTCCA
1 CCTTCCA
16790019 CCTTCCA
1 CCTTCCA
16790026 CCTT
1 CCTT
16790030 TTAGCCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.56, G:0.00, T:0.32
Consensus pattern (7 bp):
CCTTCCA
Found at i:16797911 original size:25 final size:25
Alignment explanation
Indices: 16797882--16797932 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
16797872 GAAAATAATG
*
16797882 AAGAAATATCTAGATTTCTCATGAT
1 AAGAAATATATAGATTTCTCATGAT
16797907 AAGAAATATATAGATTTCTCATGAT
1 AAGAAATATATAGATTTCTCATGAT
16797932 A
1 A
16797933 TTTCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (25 bp):
AAGAAATATATAGATTTCTCATGAT
Found at i:16798999 original size:45 final size:45
Alignment explanation
Indices: 16798923--16799040 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
16798913 TGACACAGTT
* * * * * *
16798923 CGCACGTATGAGTCCGCCATATCTATTAATCTTCTTTTATGAATC
1 CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
* *
16798968 CGTATGTATGAGTCCACTATATTTATGAATCTACTTCTATGAATC
1 CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
*
16799013 CGCATGAATGAG-CTCACTATATCTATGA
1 CGCATGTATGAGTC-CACTATATCTATGA
16799041 GTATTCTTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (45 bp):
CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
Found at i:16800575 original size:7 final size:7
Alignment explanation
Indices: 16800563--16800596 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
16800553 CAAATTAATA
*
16800563 AAATATT
1 AAATATC
16800570 AAATATC
1 AAATATC
*
16800577 AATTATC
1 AAATATC
16800584 AAATATC
1 AAATATC
16800591 AAATAT
1 AAATAT
16800597 TATTGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (7 bp):
AAATATC
Found at i:16800850 original size:39 final size:39
Alignment explanation
Indices: 16800796--16800875 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
16800786 TAACAGAAGT
16800796 TAAAAAAATTGATGGTCAATCACATAGCG-CTACGTGGCA
1 TAAAAAAATTGATGGTCAATCACATAGCGTC-ACGTGGCA
16800835 TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
1 TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
16800874 TA
1 TA
16800876 TTTTTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (39 bp):
TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
Found at i:16801004 original size:18 final size:20
Alignment explanation
Indices: 16800968--16801005 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16800958 AAAAATTCAT
*
16800968 AAAATATATATAATGTAGAA
1 AAAAAATATATAATGTAGAA
16800988 AAAAAATATA-AAT-TAGAA
1 AAAAAATATATAATGTAGAA
16801006 GAGAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAAAATATATAATGTAGAA
Found at i:16801111 original size:20 final size:19
Alignment explanation
Indices: 16801062--16801103 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
16801052 GAAATTAGTT
16801062 AAAATTAATAATA--TTATA
1 AAAATT-ATAATATTTTATA
16801080 AAAATTATAATATTTTATA
1 AAAATTATAATATTTTATA
16801099 AAAAT
1 AAAAT
16801104 ATTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTATAATATTTTATA
Found at i:16801120 original size:20 final size:19
Alignment explanation
Indices: 16801066--16801121 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
16801056 TTAGTTAAAA
16801066 TTAATAATATTATAAAAATT
1 TTAATAA-ATTATAAAAATT
* **
16801086 ATAATATTTTATAAAAATAT
1 TTAATAAATTATAAAAAT-T
*
16801106 TTAATAAATTGTAAAA
1 TTAATAAATTATAAAA
16801122 TTATGAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAATAAATTATAAAAATT
Found at i:16804341 original size:12 final size:12
Alignment explanation
Indices: 16804324--16804365 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
16804314 CCTAAGATTA
16804324 TATTTTATTATG
1 TATTTTATTATG
*
16804336 TATTTTACTAT-
1 TATTTTATTATG
16804347 TATTTTATTATG
1 TATTTTATTATG
16804359 TATTTTA
1 TATTTTA
16804366 CTATCTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (12 bp):
TATTTTATTATG
Found at i:16804350 original size:23 final size:23
Alignment explanation
Indices: 16804324--16804369 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16804314 CCTAAGATTA
16804324 TATTTTATTATGTATTTTACTAT
1 TATTTTATTATGTATTTTACTAT
16804347 TATTTTATTATGTATTTTACTAT
1 TATTTTATTATGTATTTTACTAT
16804370 CTAGTCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATTATGTATTTTACTAT
Found at i:16809443 original size:12 final size:12
Alignment explanation
Indices: 16809426--16809452 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16809416 GGTGGGAAAG
16809426 AAGTTTTCATTA
1 AAGTTTTCATTA
16809438 AAGTTTTCATTA
1 AAGTTTTCATTA
16809450 AAG
1 AAG
16809453 CTATTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (12 bp):
AAGTTTTCATTA
Found at i:16813392 original size:15 final size:15
Alignment explanation
Indices: 16813358--16813391 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16813348 TGGCATAATA
*
16813358 ATTTGCTAACTTTGT
1 ATTTTCTAACTTTGT
16813373 ATTTTCTAACTTT-T
1 ATTTTCTAACTTTGT
16813387 ATTTT
1 ATTTT
16813392 TAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTTTCTAACTTTGT
Found at i:16813547 original size:25 final size:27
Alignment explanation
Indices: 16813500--16813553 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
16813490 TTTTCATATT
* *
16813500 TTAAATAAATTTTTATA-GTTTTTATA
1 TTAAATAAATTTTTACACATTTTTATA
16813526 TTAAAT-AATTTTTACACATTTTTATA
1 TTAAATAAATTTTTACACATTTTTATA
16813552 TT
1 TT
16813554 TTTAAAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (27 bp):
TTAAATAAATTTTTACACATTTTTATA
Found at i:16815408 original size:21 final size:20
Alignment explanation
Indices: 16815384--16815433 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
16815374 TATAAACGTG
* *
16815384 AAACAACACCAAAACAGTGA
1 AAACAACACAAAAACAATGA
16815404 CAAACAACAACAAAAACAATGA
1 -AAACAAC-ACAAAAACAATGA
16815426 AAACAACA
1 AAACAACA
16815434 GCAAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.54
22 11 0.42
ACGTcount: A:0.66, C:0.24, G:0.06, T:0.04
Consensus pattern (20 bp):
AAACAACACAAAAACAATGA
Found at i:16818498 original size:17 final size:17
Alignment explanation
Indices: 16818476--16818508 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16818466 GTTGAACTAA
*
16818476 TTTTTTATA-TTTTTAT
1 TTTTTTTTAGTTTTTAT
16818492 TTTTTTTTAGTTTTTAT
1 TTTTTTTTAGTTTTTAT
16818509 GAAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTTTAGTTTTTAT
Found at i:16836631 original size:72 final size:73
Alignment explanation
Indices: 16836433--16837144 Score: 1067
Period size: 72 Copynumber: 9.7 Consensus size: 73
16836423 TGATGTTTTT
*
16836433 ATTTCTG-TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
16836497 GTAATTTCA
65 GTAATTTCA
* *
16836506 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAG
1 ATTTCTGTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
16836571 GTAATTTCA
65 GTAATTTCA
*
16836580 ATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
16836644 TAATTTCA
66 TAATTTCA
* ** * *
16836652 ATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
*
16836716 TATTTTCA
66 TAATTTCA
* *
16836724 ATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGT-TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
16836789 GGTAATTTCA
64 GGTAATTTCA
* **
16836799 ATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
16836864 GTAATTTCA
65 GTAATTTCA
* * ** * *
16836873 ATTTCTGTTTTC-AAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
*
16836937 TATTTTCA
66 TAATTTCA
* *
16836945 ATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA
1 ATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
16837010 GGTAATTTCA
64 GGTAATTTCA
* *
16837020 ATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAGACACGCTAAA
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCTGAG
16837083 GTAATTTCA
65 GTAATTTCA
*
16837092 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
16837145 ATCACACATG
Statistics
Matches: 585, Mismatches: 43, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
71 1 0.00
72 261 0.45
73 55 0.09
74 148 0.25
75 120 0.21
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (73 bp):
ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTCA
Found at i:16837038 original size:293 final size:291
Alignment explanation
Indices: 16836433--16837144 Score: 1099
Period size: 293 Copynumber: 2.4 Consensus size: 291
16836423 TGATGTTTTT
16836433 ATTTCTG-TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTC-AAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
* *
16836497 GTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
65 GTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* **
16836562 CACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
130 CACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGC
** *
16836627 CTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGA
195 CTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGA
* *
16836692 GTTGAGCCTCAAGACACGTTGAGGTATTTTCA
260 GTTGAGCCTCAAGACACGCTGAGGTAATTTCA
*
16836724 ATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGT-TTTC-AAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
**
16836789 GGTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
64 GGTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
16836854 ACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAG
129 ACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAG
* * * *
16836919 CCTCAAGACATGCTGAGGTATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAG
194 CCTCAAGACACGCTGAGGTAATTTCAATTTCTG-TTTTC--AAAAATCAACTCATATTGCGAGAA
* **
16836984 GTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCA
256 ATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
* * *
16837020 ATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAGACACGCTAAA
1 ATTTCTGTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCTGAG
* *
16837083 GTAATTTCAATTTCTGTT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
65 GTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
16837145 ATCACACATG
Statistics
Matches: 386, Mismatches: 29, Indels: 11
0.91 0.07 0.03
Matches are distributed among these distances:
291 6 0.02
292 41 0.11
293 270 0.70
294 5 0.01
295 4 0.01
296 60 0.16
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (291 bp):
ATTTCTGTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
ACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCC
TCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAG
TTGAGCCTCAAGACACGCTGAGGTAATTTCA
Found at i:16837163 original size:221 final size:219
Alignment explanation
Indices: 16836433--16837139 Score: 1132
Period size: 221 Copynumber: 3.2 Consensus size: 219
16836423 TGATGTTTTT
* ** *
16836433 ATTTCTG-TTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
* * *
16836497 GTAATTTCAATTTCTG-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
64 GTATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
16836561 ACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
129 ACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
16836626 CCTCGGGACACGCTGAGGTAATTTCA
194 CCTCGAGACACGCTGAGGTAATTTCA
* *
16836652 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
* * *
16836717 ATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGAC
66 ATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
* **
16836782 ACGCTGAGGTAATTTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAG
131 ACGCTGAGGTAATTTCAATTTCTGTT-TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
16836847 CCTC-AGGACACGCTGAGGTAATTTCA
194 CCTCGA-GACACGCTGAGGTAATTTCA
* * *
16836873 ATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACATGCTGAGGT
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
16836938 ATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
66 ATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
16837003 ACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
131 ACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
16837068 TCGAGACACGCTAAAGTAATTTCA
196 TCGAGACACGCTGAGGTAATTTCA
**
16837092 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 ATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
16837140 TTCAGATCAC
Statistics
Matches: 450, Mismatches: 31, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
218 59 0.13
219 145 0.32
220 40 0.09
221 206 0.46
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (219 bp):
ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
ATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
ACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCGAGACACGCTGAGGTAATTTCA
Found at i:16838950 original size:15 final size:17
Alignment explanation
Indices: 16838922--16838953 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16838912 TTGTATATAT
16838922 TATATTTATATTATGTA
1 TATATTTATATTATGTA
16838939 TATATTT-T-TTATGTA
1 TATATTTATATTATGTA
16838954 CGTTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATATTTATATTATGTA
Found at i:16844254 original size:3 final size:3
Alignment explanation
Indices: 16844246--16844270 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16844236 ACTAATGTAC
16844246 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
16844271 TTGAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16847100 original size:39 final size:40
Alignment explanation
Indices: 16847044--16847135 Score: 145
Period size: 39 Copynumber: 2.4 Consensus size: 40
16847034 AAATTAATAA
*
16847044 ATAAAAAATTTAAAATAAGTATGAAAAATAATTAT-TTTT
1 ATAATAAATTTAAAATAAGTATGAAAAATAATTATCTTTT
16847083 ATAATAAATTTAAAATAAGTATGAAAAATAATTATCTTTT
1 ATAATAAATTTAAAATAAGTATGAAAAATAATTATCTTTT
*
16847123 -T-ATAATTTTAAAA
1 ATAATAAATTTAAAA
16847136 ATGAAACATA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
38 11 0.22
39 35 0.70
40 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (40 bp):
ATAATAAATTTAAAATAAGTATGAAAAATAATTATCTTTT
Found at i:16848206 original size:26 final size:25
Alignment explanation
Indices: 16848177--16848240 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
16848167 CCCTCCCAAA
16848177 AAAAAACCTAACCAAAAAAAAAGAAG
1 AAAAAACCTAACCAAAAAAAAA-AAG
*
16848203 AAAAAACCTAACCCAAAAAGAAAAAG
1 AAAAAACCTAA-CCAAAAAAAAAAAG
16848229 -AAAAACCTAACC
1 AAAAAACCTAACC
16848241 CCCTCCCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 2 0.06
25 10 0.28
26 14 0.39
27 10 0.28
ACGTcount: A:0.69, C:0.20, G:0.06, T:0.05
Consensus pattern (25 bp):
AAAAAACCTAACCAAAAAAAAAAAG
Found at i:16848241 original size:25 final size:25
Alignment explanation
Indices: 16848174--16848241 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
16848164 AAGCCCTCCC
16848174 AAAA-AAAAACCTAA-CCAAAAAAA
1 AAAAGAAAAACCTAACCCAAAAAAA
*
16848197 AAGAAGAAAAAACCTAACCCAAAAAGA
1 AA-AAG-AAAAACCTAACCCAAAAAAA
16848224 AAAAGAAAAACCTAACCC
1 AAAAGAAAAACCTAACCC
16848242 CCTCCCCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 13 0.32
26 13 0.32
27 10 0.25
ACGTcount: A:0.69, C:0.21, G:0.06, T:0.04
Consensus pattern (25 bp):
AAAAGAAAAACCTAACCCAAAAAAA
Found at i:16850774 original size:11 final size:12
Alignment explanation
Indices: 16850751--16850785 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
16850741 ATTCATTTGA
16850751 CATTCATGCATT
1 CATTCATGCATT
16850763 CATTCATG-ATT
1 CATTCATGCATT
*
16850774 CATTCATACATT
1 CATTCATGCATT
16850786 GCATATCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.43
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:16859318 original size:117 final size:109
Alignment explanation
Indices: 16859118--16859332 Score: 290
Period size: 109 Copynumber: 1.9 Consensus size: 109
16859108 GGTATTTTTA
16859118 TTTTTTTTCAAATCAACTCATATTGCGAGAAGTGAGTTGAGCTCGGGCCGCTGAGTATTTTTTTT
1 TTTTTTTTCAAATCAACTCATATTGCGAGAAGTGAGTTGAGCTCGGGCCGCTGAGTATTTTTTTT
*
16859183 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTAAT
66 TTTTAAATTAACTCATATTGCGAGAGGTGAGTTAAGCTTTTAAT
* *
16859227 TTTTTTTTCAAATCAACTCATATTGCTAG-AGTGA-TTGAGCCTCGAGGCATGCTGAGTATTTTC
1 TTTTTTTTCAAATCAACTCATATTGCGAGAAGTGAGTTGAG-CTCG-GGC-CGCTGAGTA-TTT-
*
16859290 AATTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTT
61 --TTTT-T-TTTTAAATT-AACTCATATTGCGAGAGGTGAGTT
16859333 GAGCCTCAGG
Statistics
Matches: 92, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
107 5 0.05
108 9 0.10
109 31 0.34
110 8 0.09
111 3 0.03
114 4 0.04
115 1 0.01
116 8 0.09
117 23 0.25
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (109 bp):
TTTTTTTTCAAATCAACTCATATTGCGAGAAGTGAGTTGAGCTCGGGCCGCTGAGTATTTTTTTT
TTTTAAATTAACTCATATTGCGAGAGGTGAGTTAAGCTTTTAAT
Found at i:16859393 original size:73 final size:70
Alignment explanation
Indices: 16859224--16859407 Score: 191
Period size: 73 Copynumber: 2.6 Consensus size: 70
16859214 TTAAGCTTTT
* * * *
16859224 AATTTT-TTTTTC-AAATCAACTCATATTGCTAGA-GTGA-TTGAGCCTCGAGGCATGCTGAGTA
1 AATTTTGTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGATGAGTA
* *
16859285 TTTTC
66 ATCTC
* **
16859290 AATTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGATGAGG
1 AATTTTGTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGG-CACGATGA-G
16859354 TAATCTC
64 TAATCTC
*
16859361 AATTTCTGT-TTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 AATTT-TGTGTT-TCAA-AATCAACTCATATTGCGAGAGGTGAGTTGA
16859408 ACCTTTTAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
66 6 0.06
67 4 0.04
68 18 0.19
69 7 0.07
70 15 0.16
71 13 0.14
72 6 0.06
73 27 0.28
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (70 bp):
AATTTTGTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGATGAGTA
ATCTC
Found at i:16859686 original size:14 final size:13
Alignment explanation
Indices: 16859653--16859686 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16859643 CGTCAAGGTA
16859653 TTTTCAATTTCCG
1 TTTTCAATTTCCG
*
16859666 TTTTCAATTTCTG
1 TTTTCAATTTCCG
16859679 TCTTTCAA
1 T-TTTCAA
16859687 AAAATCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (13 bp):
TTTTCAATTTCCG
Found at i:16859696 original size:89 final size:84
Alignment explanation
Indices: 16859430--16859732 Score: 360
Period size: 89 Copynumber: 3.5 Consensus size: 84
16859420 CTACTTTTTC
* * * *
16859430 AAAATCAGCTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCATGCAATGTATTTTTAATTTCTG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCAAGGTA-TTTTAATTTCTG
*
16859495 TCTTCATTTTATGTTTTGAA
65 TTTTCATTTTATGTTTTGAA
* * *
16859515 AGAATCAGCT--TATTGCGAGAGGTGAGTTGAG-CTCAGGTCACGCCGAGGTATTTTAATTTCTG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG-CAAGGTATTTTAATTTCTG
16859577 TTTTCATTATTATGTTTTGAA
65 TTTTCATT-TTATGTTTTGAA
* * *
16859598 AGAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCAAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT--CACG-CAAGGTATTTT-AATTT
* * * *
16859663 CCGTTTTCAATTTCTGTCTTTCAA
62 CTGTTTTCATTTTATGT-TTTGAA
* *
16859687 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACACGC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
16859733 TGAGGTAATT
Statistics
Matches: 190, Mismatches: 19, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
82 29 0.15
83 46 0.24
85 29 0.15
86 8 0.04
87 4 0.02
88 19 0.10
89 55 0.29
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (84 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCAAGGTATTTTAATTTCTGT
TTTCATTTTATGTTTTGAA
Found at i:16859788 original size:72 final size:72
Alignment explanation
Indices: 16859685--16859821 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
16859675 TCTGTCTTTC
* * *
16859685 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGG-ACACGCTGAGGTAATTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACACGCCGAGGT-ATTTCAATT
16859749 CTGTGTCA
65 CTGTGTCA
* *
16859757 AAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-CACACGCCGAGGTATTTCAATT
16859822 TCCGTTTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
72 38 0.66
73 9 0.16
74 11 0.19
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (72 bp):
AAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACACGCCGAGGTATTTCAATTC
TGTGTCA
Found at i:16859875 original size:160 final size:160
Alignment explanation
Indices: 16859600--16859987 Score: 631
Period size: 160 Copynumber: 2.4 Consensus size: 160
16859590 GTTTTGAAAG
* *
16859600 AATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCAAGGTATTTTCAATTTCC
1 AATCAACTCGTATTGCGAG-GGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCC
* *
16859665 GTTTTCAATTTCTGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACA
65 GTTTTCAATTTCTGCCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
16859730 CGCTGAGGTAATTTCAATTCTGTGTCAAAAA
130 CACTGAGGTAATTTCAATTCTGTGTCAAAAA
16859761 AATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTA-TTTCAATTTCC
1 AATCAACTCGTATTGCGAG-GGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCC
**
16859825 GTTTTCAATTTC-GCCTTTCAAAAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
65 GTTTTCAATTTCTGCCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
16859889 ACACTGAGGTAATTTCAATTCTGTGTCAAAAA
129 ACACTGAGGTAATTTCAATTCTGTGTCAAAAA
* * *
16859921 AATCAACTCGTATTGCGAGCGCGAG-TGAGCCTTAGGTCA-ACGCCGAGGTATTTTCAATTTCTG
1 AATCAACTCGTATTGCGAGGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCG
16859984 TTTT
66 TTTT
16859988 TCAAAAAAAA
Statistics
Matches: 214, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
157 11 0.05
158 28 0.13
159 11 0.05
160 114 0.53
161 50 0.23
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (160 bp):
AATCAACTCGTATTGCGAGGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCG
TTTTCAATTTCTGCCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
ACTGAGGTAATTTCAATTCTGTGTCAAAAA
Found at i:16870049 original size:1 final size:1
Alignment explanation
Indices: 16870043--16870079 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
16870033 CGTGATAACT
16870043 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16870080 GGTTAACTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16870291 original size:166 final size:182
Alignment explanation
Indices: 16870064--16870411 Score: 500
Period size: 167 Copynumber: 2.0 Consensus size: 182
16870054 AAAAAAAAAA
16870064 AAAAAAAAAAAAAAAAGGTTAACTCACCTCTGCAATATGAGTCAATTTAAAACATAAACT-AAAA
1 AAAAAAAAAAAAAAAAGGTTAACTCACCTC-GCAATATGAGTCAATTTAAAACATAAACTAAAAA
*
16870128 TACCTCGGCGTGCCCCGA-GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-TAAAAAATT-
65 TACCTCGGCGTG-CCCGAGGCTCAACTCACTTCTCG-AATATGAGTTGATTTTTAAAAAAAATTA
16870190 AAAA-ACCTCAACGT-TC-TGA-G-TCAAC-CATT-TCGCAA-ATGAG-TGATTG
128 AAAATACCTCAACGTGTCTTGAGGCTCAACTCATTCTCGCAATATGAGTTGATTG
**
16870236 AAAAAAAAAATTAAAAGGCTTAA-TCACCTC-C-A-ATGA-TCAATTT-AAACATAAACTAAAAA
1 AAAAAAAAAAAAAAAAGG-TTAACTCACCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAA
16870295 TACCTCGGCGTGCCCGAGGCTCAACTCACTTCTCGAATATGAGTTGATTTTTAAAAAAAATTAAA
65 TACCTCGGCGTGCCCGAGGCTCAACTCACTTCTCGAATATGAGTTGATTTTTAAAAAAAATTAAA
16870360 AATACCTCAACGTGTCTTGAGGCTCAACTCATTCTCGCAATATGAGTTGATT
130 AATACCTCAACGTGTCTTGAGGCTCAACTCATTCTCGCAATATGAGTTGATT
16870412 TTCCTTGGAA
Statistics
Matches: 159, Mismatches: 3, Indels: 23
0.86 0.02 0.12
Matches are distributed among these distances:
166 33 0.21
167 48 0.30
168 8 0.05
169 11 0.07
170 3 0.02
171 3 0.02
172 24 0.15
173 9 0.06
174 4 0.03
175 6 0.04
176 5 0.03
177 5 0.03
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (182 bp):
AAAAAAAAAAAAAAAAGGTTAACTCACCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAAT
ACCTCGGCGTGCCCGAGGCTCAACTCACTTCTCGAATATGAGTTGATTTTTAAAAAAAATTAAAA
ATACCTCAACGTGTCTTGAGGCTCAACTCATTCTCGCAATATGAGTTGATTG
Found at i:16878599 original size:34 final size:33
Alignment explanation
Indices: 16878525--16878636 Score: 88
Period size: 34 Copynumber: 3.3 Consensus size: 33
16878515 TTTCCTTTTT
* * *
16878525 TTTTG-AACACAATTTTTTTAAAATACA--AGAA
1 TTTTGAAACACAA-ATTTTTAAAAAACACGAAAA
16878556 TTTTAGAAACACAAATTTTTAAAAAAACACGAAAA
1 TTTT-GAAACACAAATTTTT-AAAAAACACGAAAA
* **
16878591 TTTTGAAACACGAGATTTCTT-TGAAACACGAAAA
1 TTTTGAAACAC-AAATTT-TTAAAAAACACGAAAA
16878625 TTTATGAAACAC
1 TTT-TGAAACAC
16878637 GGTCAATTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
31 4 0.06
32 6 0.09
33 14 0.21
34 21 0.31
35 20 0.30
36 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (33 bp):
TTTTGAAACACAAATTTTTAAAAAACACGAAAA
Found at i:16878634 original size:17 final size:17
Alignment explanation
Indices: 16878580--16878931 Score: 189
Period size: 17 Copynumber: 19.9 Consensus size: 17
16878570 ATTTTTAAAA
16878580 AAACACGAAAA-TTTTG
1 AAACACGAAAATTTTTG
* *
16878596 AAACACGAGATTTCTTTG
1 AAACACGAAAATT-TTTG
*
16878614 AAACACGAAAATTTATG
1 AAACACGAAAATTTTTG
** *
16878631 AAACACGGTCAATTTCTTA
1 AAACAC-GAAAATTT-TTG
* *
16878650 AAACGCGAAAGTTTTTGG
1 AAACACGAAAATTTTT-G
**
16878668 AAA-ACGGGAATTTTTTTTTG
1 AAACAC--GAA--AATTTTTG
*
16878688 AAACACGAAAAATTTTG
1 AAACACGAAAATTTTTG
*
16878705 AAACACTG-GAA-TTTTG
1 AAACAC-GAAAATTTTTG
** *
16878721 AAAACACGAGGATTTTTT
1 -AAACACGAAAATTTTTG
* *
16878739 AAATACGAAAA-ATTTG
1 AAACACGAAAATTTTTG
*
16878755 AAAACAAGAAAATTTTTG
1 -AAACACGAAAATTTTTG
* *
16878773 AAATACGAAAATTTTAG
1 AAACACGAAAATTTTTG
16878790 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
16878807 AAACAC-AGAAGTTTTTAG
1 AAACACGA-AAATTTTT-G
*
16878825 AAAACACGAAAAATTTTG
1 -AAACACGAAAATTTTTG
* **
16878843 AAA-ATTGGAATTTTTTTG
1 AAACA--CGAAAATTTTTG
*
16878861 AAAACACGAGAATTTTTG
1 -AAACACGAAAATTTTTG
*
16878879 AAAAACATGAAAATTTTTG
1 --AAACACGAAAATTTTTG
* *
16878898 CAACAC-AGGAATTTTTG
1 AAACACGA-AAATTTTTG
16878915 AAAACACGAAAAATTTT
1 -AAACACG-AAAATTTT
16878932 CCGATTTTTA
Statistics
Matches: 253, Mismatches: 54, Indels: 55
0.70 0.15 0.15
Matches are distributed among these distances:
16 21 0.08
17 108 0.43
18 61 0.24
19 49 0.19
20 7 0.03
21 7 0.03
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:16879069 original size:21 final size:21
Alignment explanation
Indices: 16879035--16879077 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
16879025 TGTTACCTTA
*
16879035 TTTTTGAAAAACACGAGAAATT
1 TTTTTGAAAAACAC-AAAAATT
*
16879057 TTTTTG-AAGACACAAAAATT
1 TTTTTGAAAAACACAAAAATT
16879077 T
1 T
16879078 CGAAACCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (21 bp):
TTTTTGAAAAACACAAAAATT
Found at i:16879300 original size:8 final size:6
Alignment explanation
Indices: 16879244--16879297 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
16879234 AAATTATTTA
* *
16879244 AAATA- AAATA- AAATAA AAAT-T AAAT-T AAATTAA AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAA-TAT AAATAT AAATAT
16879289 AAATAT AAA
1 AAATAT AAA
16879298 AATGCATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
5 18 0.42
6 22 0.51
7 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATAT
Found at i:16879466 original size:13 final size:11
Alignment explanation
Indices: 16879438--16879478 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
16879428 AACCTCTTTT
16879438 TTCTTTTTTCC
1 TTCTTTTTTCC
16879449 TTCTTTTTTCC
1 TTCTTTTTTCC
16879460 TTCTCTTTTT-C
1 TTCT-TTTTTCC
16879471 TTCTTTTT
1 TTCTTTTT
16879479 CTTTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.14
11 20 0.69
12 5 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTTTTTTCC
Found at i:16879485 original size:22 final size:20
Alignment explanation
Indices: 16879434--16879494 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 20
16879424 ATTGAACCTC
16879434 TTTTTTCTTTTTTCCTTCTTT
1 TTTTTTCTTTTTT-CTTCTTT
*
16879455 TTTCCTTCTCTTTTTCTTCTTT
1 TTT-TTTCT-TTTTTCTTCTTT
16879477 TTCTTTTCTTTTTT-TTCT
1 TT-TTTTCTTTTTTCTTCT
16879495 CTGCTGGGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 4 0.11
21 8 0.23
22 17 0.49
23 6 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTTCTTT
Found at i:16879661 original size:6 final size:6
Alignment explanation
Indices: 16879652--16879678 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16879642 GGCTTGTTTC
16879652 TTTTTG TTTTTG TTTTTG TTTTTG TTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTT
16879679 CTTTTTCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:16880229 original size:29 final size:29
Alignment explanation
Indices: 16880196--16880312 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
16880186 TGTAATTTTT
*
16880196 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
16880225 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
16880255 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
16880284 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
16880313 TTATTTTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:16880251 original size:30 final size:30
Alignment explanation
Indices: 16880211--16880312 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
16880201 ATTTAGGATT
*
16880211 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
16880241 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
16880271 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
16880301 AAAATGCAATTT
1 AAAATGAAATTT
16880313 TTATTTTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:16880332 original size:13 final size:14
Alignment explanation
Indices: 16880308--16880340 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
16880298 GTCAAAATGC
*
16880308 AATTTTTATTTTTA
1 AATTTTTATTTTGA
16880322 AATTTTT-TTTTGA
1 AATTTTTATTTTGA
16880335 AATTTT
1 AATTTT
16880341 GAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
AATTTTTATTTTGA
Found at i:16881861 original size:23 final size:22
Alignment explanation
Indices: 16881835--16881888 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
16881825 GTAAATCGCC
16881835 TTATATACTTTTCAAA-ATTCTAT
1 TTATATA-TTTT-AAAGATTCTAT
*
16881858 TTATTTATTTTAAAGTATTCTAT
1 TTATATATTTTAAAG-ATTCTAT
16881881 TTAT-TATT
1 TTATATATT
16881889 CATTATAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 8 0.29
23 17 0.61
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATATATTTTAAAGATTCTAT
Found at i:16881989 original size:27 final size:27
Alignment explanation
Indices: 16881933--16881987 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
16881923 TTTATGTACA
* *
16881933 TATATGTATATTACTTGTTCTAAAATT
1 TATATATATATCACTTGTTCTAAAATT
* *
16881960 TATATATATATCATCTTTTTCTTAAATT
1 TATATATATATCA-CTTGTTCTAAAATT
16881988 ATTTTATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.55
Consensus pattern (27 bp):
TATATATATATCACTTGTTCTAAAATT
Found at i:16889595 original size:23 final size:23
Alignment explanation
Indices: 16889569--16889622 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
16889559 GTAAATCGCC
*
16889569 TTATATACTTTTCAAA-ATTCTAT
1 TTATATA-TTTTAAAATATTCTAT
*
16889592 TTATTTATTTTAAAATATTCTAT
1 TTATATATTTTAAAATATTCTAT
16889615 TTAT-TATT
1 TTATATATT
16889623 CATTATAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATATATTTTAAAATATTCTAT
Found at i:16889622 original size:22 final size:22
Alignment explanation
Indices: 16889577--16889619 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16889567 CCTTATATAC
*
16889577 TTTTCAAAATTCTATTTATTTA
1 TTTTAAAAATTCTATTTATTTA
16889599 TTTTAAAATATTCTATTTATT
1 TTTTAAAA-ATTCTATTTATT
16889620 ATTCATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAAATTCTATTTATTTA
Found at i:16889723 original size:27 final size:27
Alignment explanation
Indices: 16889667--16889721 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
16889657 TTTATGTACA
* *
16889667 TATATGTATATTACTTGTTCTAAAATT
1 TATATATATATCACTTGTTCTAAAATT
* *
16889694 TATATATATATCATCTTTTTCTTAAATT
1 TATATATATATCA-CTTGTTCTAAAATT
16889722 ATTTTATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.55
Consensus pattern (27 bp):
TATATATATATCACTTGTTCTAAAATT
Found at i:16896873 original size:16 final size:17
Alignment explanation
Indices: 16896839--16896882 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
16896829 ATGATTTTCT
16896839 CTAAACCC-T-AATGCA
1 CTAAACCCTTAAATGCA
16896854 CTAAACCCTTAAAT-CA
1 CTAAACCCTTAAATGCA
*
16896870 CTAAACCTTTAAA
1 CTAAACCCTTAAA
16896883 CCCTTAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.31
16 15 0.58
17 3 0.12
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.25
Consensus pattern (17 bp):
CTAAACCCTTAAATGCA
Found at i:16896958 original size:14 final size:14
Alignment explanation
Indices: 16896934--16896967 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16896924 AACCCATTAA
*
16896934 CCCTGACTCCTAAC
1 CCCTAACTCCTAAC
*
16896948 TCCTAACTCCTAAC
1 CCCTAACTCCTAAC
16896962 CCCTAA
1 CCCTAA
16896968 ACCCTAAACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.47, G:0.03, T:0.24
Consensus pattern (14 bp):
CCCTAACTCCTAAC
Found at i:16896973 original size:14 final size:15
Alignment explanation
Indices: 16896939--16896985 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
16896929 ATTAACCCTG
*
16896939 ACTCCTAACTCCT-A
1 ACTCCTAACCCCTAA
16896953 ACTCCTAACCCCTAA
1 ACTCCTAACCCCTAA
*
16896968 AC-CCTAAACCCATAA
1 ACTCCT-AACCCCTAA
16896983 ACT
1 ACT
16896986 ATAGGCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (15 bp):
ACTCCTAACCCCTAA
Found at i:16897017 original size:28 final size:29
Alignment explanation
Indices: 16896973--16897040 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
16896963 CCTAAACCCT
*
16896973 AAACCCATAAACTATAGGCTTTAAATCTC
1 AAACCCATAAACTATAGGCCTTAAATCTC
16897002 AAACCC-TAAACTATAGGCCTTAAATCTC
1 AAACCCATAAACTATAGGCCTTAAATCTC
*
16897030 AAA-TCATAAAC
1 AAACCCATAAAC
16897041 CTTAAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 1 0.03
28 29 0.81
29 6 0.17
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (29 bp):
AAACCCATAAACTATAGGCCTTAAATCTC
Found at i:16897565 original size:42 final size:42
Alignment explanation
Indices: 16897500--16897639 Score: 122
Period size: 42 Copynumber: 3.5 Consensus size: 42
16897490 TAAAATTTAT
*
16897500 GTTTAAGGT-TTAGGGTATT-GGGTTCAGGATTTAGTTTATAAG
1 GTTTAAGGTATTAGGGTATTAGGGTT-AGG-TTTAGTCTATAAG
16897542 GTTTAAGGTATT-GGGT-TTA--G---GGTTTAGTCTATAAG
1 GTTTAAGGTATTAGGGTATTAGGGTTAGGTTTAGTCTATAAG
* * *
16897577 GTTTAGGGTATT-GGGTATTAGGTTTAAGGTTTAGTCTATATG
1 GTTTAAGGTATTAGGGTATTAGGGTT-AGGTTTAGTCTATAAG
* *
16897619 GTTTATGGTATTGGGGT-TTAG
1 GTTTAAGGTATTAGGGTATTAG
16897640 TCTATTGGTT
Statistics
Matches: 83, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
35 27 0.33
36 5 0.06
40 1 0.01
41 2 0.02
42 42 0.51
43 6 0.07
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.44
Consensus pattern (42 bp):
GTTTAAGGTATTAGGGTATTAGGGTTAGGTTTAGTCTATAAG
Found at i:16897579 original size:21 final size:21
Alignment explanation
Indices: 16897555--16897623 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
16897545 TAAGGTATTG
16897555 GGTTTAGGGTTTAGTCTATAA
1 GGTTTAGGGTTTAGTCTATAA
** *
16897576 GGTTTAGGGTATT-GGGTATTA
1 GGTTTAGGGT-TTAGTCTATAA
* *
16897597 GGTTTAAGGTTTAGTCTATAT
1 GGTTTAGGGTTTAGTCTATAA
16897618 GGTTTA
1 GGTTTA
16897624 TGGTATTGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.45
Consensus pattern (21 bp):
GGTTTAGGGTTTAGTCTATAA
Done.